Extracellular oxidoreduction potential modifies carbon and electron flow in Escherichia coli

Impact of kdcA, pdhD, and codY gene regulation in Lactococcus lactis 408 on 3-methylbutanal formation during cheddar cheese ripening

3-Methylbutanal, a key volatile compound contributing to the nutty flavor of cheese, was primarily produced through the microbial catabolism of leucine. This study focused on the metabolic pathway of 3-methylbutanal at the genetic level during the ripening of Cheddar cheese. The influence of key genes (kdcA, pdhD, and codY) in Lactococcus lactis 408, a specifically selected adjunct culture, on the production of 3-methylbutanal was evaluated. Over a 14-day ripening period, a minor difference in leucine production was observed among different samples with adjunct culture, while alterations in the genes kdcA and pdhD, which were overexpressed in the strain, led to a decreased concentration of α-ketoisocaproate. Utilizing headspace solid-phase microextraction coupled with gas chromatography-flame ionization detection, a reduction was observed in 3-methylbutanal levels as ripening progressed. However, cheese fermented with the codY knockout strain displayed the highest level of 3-methylbutanal at both 0.5-day and 28-day ripening milestones. Further analysis using an Ag/AgCl electrode to assess the redox environment revealed that the higher redox potential in the codY knockout strain was instrumental in retaining elevated levels of 3-methylbutanal. These findings underscored the critical role of genetic factors in the flavor development of cheese and offered promising targets for enhancing flavor profiles in dairy products through biotechnological interventions.

Designing synthetic microbial communities for enhanced anaerobic waste treatment

Synthetic microbial communities (SynComs) are powerful tools for investigating microbial interactions and community assembly by focusing on minimal yet functionally representative members. Here, we will highlight key principles for designing SynComs, specifically emphasizing the anaerobic digestion (AD) microbiome for waste treatment and upcycling. The AD process has traditionally been used to reduce organic waste volume while producing biogas as a renewable energy source. Its microbiome features well-defined trophic layers and metabolic groups. There has been growing interest in repurposing the AD process to produce value-added products and chemical precursors, contributing to sustainable waste management and the goals of a circular economy. Optimizing the AD process requires a better understanding of microbial interactions and the influence of both biotic and abiotic parameters, where SynComs offer great promise. Focusing on AD microbiomes, we review the principles of SynComs' design, including keystone taxa and function, cross-feeding interactions, and metabolic redundancy, as well as how modeling approaches could guide SynComs design. Furthermore, we address practical considerations for working with AD SynComs and examine constructed SynComs designed for anaerobic waste digestion. Finally, we discuss the challenges associated with designing and applying SynComs to enhance our understanding of the AD process. This review aims to explore the use of synthetic communities in studying anaerobic digestion and highlights their potential for developing innovative biotechnological processes.

Selective butyrate production from CO2 and methanol in microbial electrosynthesis - influence of pH

Methanol assisted microbial electrosynthesis (MES) enables butyrate production from carbon dioxide and methanol using external electricity. However, the effects of operational parameters on butyrate formation remain unclear. By running three flat plate MES reactors with fed-batch mode at three controlled pH values (5.5, 6 and 7), the present study investigated the influence of pH on methanol assisted MES by comparing the process performance, microbial community structure, and genetic potential. The highest butyrate selectivity (87 % on carbon basis) and the highest butyrate production rate of 0.3 g L-1 d-1 were obtained at pH 6. At pH 7, a comparable butyrate production rate was achieved, yet with a lower selectivity (70 %) accompanied with acetate production. Butyrate production rate was considerably hindered at pH 5.5, reaching 0.1 g L-1 d-1, while the selectivity reached was up to 81 %. Methanol and CO2 consumption increased with pH, along with more negative cathodic potential and more negative redox potential. Furthermore, pH affected the thermodynamical feasibility of involved reactions. The results of metagenomic analyses suggest that Eubacterium callanderi dominated the microbial communities at all pH values, which was responsible for methanol and CO2 assimilation via the Wood-Ljungdahl pathway and was likely the main butyrate producer via the reverse β-oxidation pathway.

Enhancement of methane production in anaerobic digestion of high salinity organic wastewater: The synergistic effect of nano-magnetite and potassium ions

During high salinity organic wastewater (HSOW) anaerobic digestion treatment, the process of methanogenesis can be severely inhibited in the high salinity environment, and the accumulation of volatile organic acids (VFAs) leads to failure of the anaerobic reaction. In this study, nano-magnetite and KCl were adopted to alleviate the inhibitory effect of high salinity and enhance the HSOW anaerobic digestion performance. The result showed that, under the optimal dosage of 200 mg/L, nano-magnetite addition promoted the anaerobic digestion performance, and the methane production increased by 11.06%. When KCl was added with a dosage of 0.174%, the methane production increased by 98.37%. The simultaneous addition of nano-magnetite (200 mg/L) and KCl showed a synergistic effect on enhancing HSOW anaerobic digestion performance, and the methane production increased by 124.85%. The addition of nano-magnetite and KCl promoted the conversion of VFAs, especially accelerated the degradation of propionic acid and butyric acid, also it promoted the activity of acetate kinase, dehydrogenase and F₄₂₀, and thereby enhanced the methanogenesis process. This study could provide a new method for enhancing the anaerobic digestion of HSOW.

Bioinformatics and metabolic flux analysis highlight a new mechanism involved in lactate oxidation in Clostridium tyrobutyricum

Climate change and environmental issues compel us to find alternatives to the production of molecules of interest from petrochemistry. This study aims at understanding the production of butyrate, hydrogen, and CO₂ from the oxidation of lactate with acetate in Clostridium tyrobutyricum and thus proposes an alternative carbon source to glucose. This specie is known to produce more butyrate than the other butyrate-producing clostridia species due to a lack of solvent genesis phase. The recent discoveries on flavin-based electron bifurcation and confurcation mechanism as a mode of energy conservation led us to suggest a new metabolic scheme for the formation of butyrate from lactate-acetate co-metabolism. While searching for genes encoding for EtfAB complexes and neighboring genes in the genome of C. tyrobutyricum, we identified a cluster of genes involved in butyrate formation and another cluster involved in lactate oxidation homologous to Acetobacterium woodii. A phylogenetic approach encompassing other butyrate-producing and/or lactate-oxidizing species based on EtfAB complexes confirmed these results. A metabolic scheme on the production of butyrate, hydrogen, and CO₂ from the lactate-acetate co-metabolism in C. tyrobutyricum was constructed and then confirmed with data of steady-state continuous culture. This in silico metabolic carbon flux analysis model showed the coherence of the scheme from the carbon recovery, the cofactor ratio, and the ATP yield. This study improves our understanding of the lactate oxidation metabolic pathways and the role of acetate and intracellular redox balance, and paves the way for the production of molecules of interest as butyrate and hydrogen with C. tyrobutyricum.

Enhancing menaquinone-7 biosynthesis by adaptive evolution of Bacillus natto through chemical modulator

Menaquinone-7 (MK-7) is a kind of vitamin K2 playing an important role in the treatment and prevention of cardiovascular disease, osteoporosis and arterial calcification. The purpose of this study is to establish an adaptive evolution strategy based on a chemical modulator to improve MK-7 biosynthesis in Bacillus natto. The inhibitor of 5-enolpyruvylshikimate-3-phosphate synthase (EPSP synthase), glyphosate, was chosen as the chemical modulator to perform the experiments. The final strain ALE-25-40, which was obtained after 40 cycles in 25 mmol/L glyphosate, showed a maximal MK-7 titer of 62 mg/L and MK-7 productivity of 0.42 mg/(L h), representing 2.5 and 3 times the original strain, respectively. Moreover, ALE-25-40 generated fewer spores and showed a higher NADH and redox potential. Furthermore, the mechanism related to the improved performance of ALE-25-40 was investigated by comparative transcriptomics analysis. Genes related to the sporation formation were down-regulated. In addition, several genes related to NADH formation were also up-regulated. This strategy proposed here may provide a new and alternative directive for the industrial production of vitamin K2.

Integrated strategy of CRISPR-Cas9 gene editing and small RNA RhyB regulation in Enterobacter aerogenes: A novel protocol for improving biohydrogen production

Dark fermentation is considered as one of the most practical biological hydrogen production methods. However, current productivity and yield are still not economically viable for industrial applications. This biological process must be improved through multiple strategies, of which screening for more effective microbial strains is an important aspect. Here, based on the hydrogen production pathway of E. aerogenes, we describe three strategies to improve hydrogen production by effectively regulating the anaerobic metabolism of E. aerogenes through genetic modification. This protocol describes in detail how to obtain NADH dehydrogenase-damaged mutants and overexpress Nad synthase genes using the CRISPR-Cas9 gene editing system. In addition, the overexpression of small RNA RyhB was achieved and verified by Northern Blot. This protocol is of great significance for the study of genetic engineering operation in E. aerogenes and other bacteria, and also provides theoretical guidance and technical support for the study of E. aerogenes biological hydrogen production.

Control of redox potential in a novel continuous bioelectrochemical system led to remarkable metabolic and energetic responses of Clostridium pasteurianum grown on glycerol

BACKGROUND

Electro-fermentation (EF) is an emerging tool for bioprocess intensification. Benefits are especially expected for bioprocesses in which the cells are enabled to exchange electrons with electrode surfaces directly. It has also been demonstrated that the use of electrical energy in BES can increase bioprocess performance by indirect secondary effects. In this case, the electricity is used to alter process parameters and indirectly activate desired pathways. In many bioprocesses, oxidation-reduction potential (ORP) is a crucial process parameter. While C. pasteurianum fermentation of glycerol has been shown to be significantly influenced electrochemically, the underlying mechanisms are not clear. To this end, we developed a system for the electrochemical control of ORP in continuous culture to quantitatively study the effects of ORP alteration on C. pasteurianum by metabolic flux analysis (MFA), targeted metabolomics, sensitivity and regulation analysis.

RESULTS

In the ORP range of -462 mV to -250 mV, the developed algorithm enabled a stable anodic electrochemical control of ORP at desired set-points and a fixed dilution rate of 0.1 h-1. An overall increase of 57% in the molar yield for 1,3-propanediol was observed by an ORP increase from -462 to -250 mV. MFA suggests that C. pasteurianum possesses and uses cellular energy generation mechanisms in addition to substrate-level phosphorylation. The sensitivity analysis showed that ORP exerted its strongest impact on the reaction of pyruvate-ferredoxin-oxidoreductase. The regulation analysis revealed that this influence is mainly of a direct nature. Hence, the observed metabolic shifts are primarily caused by direct inhibition of the enzyme upon electrochemical production of oxygen. A similar effect was observed for the enzyme pyruvate-formate-lyase at elevated ORP levels.

CONCLUSIONS

The results show that electrochemical ORP alteration is a suitable tool to steer the metabolism of C. pasteurianum and increase product yield for 1,3-propanediol in continuous culture. The approach might also be useful for application with further anaerobic or anoxic bioprocesses. However, to maximize the technique's efficiency, it is essential to understand the chemistry behind the ORP change and how the microbial system responds to it by transmitted or direct effects.

Effects of Individual and Block Freezing on the Quality of Pacific Oyster (Crassostrea gigas) during Storage under Different Pretreatment Conditions

In this study, a series of pretreatments, including ice-glazing, polyphosphate impregnated, and both ice-glazing and polyphosphate impregnated, were employed to pretreat shucked oysters in order to explore the optimal processing conditions for long-time storage. The effect of repeated freezing-thawing cycles on the quality of oysters was evaluated. Several quality indicators were used to investigate the effects of pretreatment. For the VBN (volatile salt-based nitrogen) value, the lowest value was 9.1 ± 0.2 of BPG (block oyster with polyphosphate impregnated and ice-glazing), which was significantly lower than 9.6 ± 0.2 of IPG (individual oyster with polyphosphate impregnated and ice-glazing). In terms of drip loss, there was no significant difference between the IPG (21.0 ± 0.2%) and the BPG (20.8 ± 0.2%). In addition, the highest WHC% (water holding capacity) was IPG (65.5 ± 0.5%) which was slightly lower than BPG (67.6 ± 0.6%). As compared to the experimental control, the IPG and BPG had the best appearance and color. In terms of TAPC (total aerobic plate count), with the increase of freezing storage time, each group showed a slight downward trend, but the difference was not statistically significant. After repeated freezing-thawing of block frozen oysters, there were significant differences in drip loss, WHC, and cooked taste with the increasing number of times, and there was a trend of deterioration (p < 0.05). Repeated freezing and thawing can seriously degrade the quality of oysters, so individual freezing (especially IPG) should be the most appropriate processing method.

Electro-fermentation: Sustainable bioproductions steered by electricity

The market of biobased products obtainable via fermentation processes is steadily increasing over the past few years, driven by the need to create a decarbonized economy. To date, industrial fermentation (IF) employs either pure or mixed microbial cultures (MMC) whereby the type of the microbial catalysts and the used feedstock affect metabolic pathways and, in turn, the type of product(s) generated. In many cases, especially when dealing with MMC, the economic viability of IF is hindered by factors such as the low attained product titer and selectivity, which ultimately challenge the downstream recovery and purification steps. In this context, electro-fermentation (EF) represents an innovative approach, based on the use of a polarized electrode interface to trigger changes in the rate, yield, titer or product distribution deriving from traditional fermentation processes. In principle, the electrode in EF can act as an electron acceptor (i.e., anodic electro-fermentation, AEF) or donor (i.e., cathodic electro-fermentation, CEF), or simply as a mean to control the oxidation-reduction potential of the fermentation broth. However, the molecular and biochemical basis underlying the EF process are still largely unknown. This review paper provides a comprehensive overview of recent literature studies including both AEF and CEF examples with either pure or mixed microbial cultures. A critical analysis of biochemical, microbiological, and engineering aspects which presently hamper the transition of the EF technology from the laboratory to the market is also presented.

Optimization of bioprocesses with Brewers' spent grain and Cellulomonas uda

Brewers' spent grain (BSG) is a low-value by-product of the brewing process, which is produced in large quantities every year. In this study, the lignocellulosic feedstock (solid BSG) was used to optimize fermentations with Cellulomonas uda. Under aerobic conditions, maximum cellulase activities of 0.98 nkat∙mL-1, maximum xylanase activities of 5.00 nkat∙mL-1 and cell yields of 0.22 gCells∙gBSG -1 were achieved. Under anaerobic conditions, enzyme activities and cell yields were lower, but valuable liquid products (organic acids, ethanol) were produced with a yield of 0.41 gProd∙gBSG -1. The growth phase of the organisms was monitored by measuring extracellular concentrations of two fluorophores pyridoxin (aerobic) and tryptophan (anaerobic) and by cell count. By combining reductive with anaerobic conditions, the ratio of ethanol to acetate was increased from 1.08 to 1.59 molEtOH∙molAc -1. This ratio was further improved to 9.2 molEtOH∙molAc -1 by lowering the pH from 7.4 to 5.0 without decreasing the final ethanol concentration. A fermentation in a bioreactor with 15 w% BSG instead of 5 w% BSG quadrupled the acetate concentration, whilst ethanol was removed by gas stripping. This study provides various ideas for optimizing and monitoring fermentations with solid substrates, which can support feasibility and incorporation into holistic biorefining approaches in the future.

HyfF subunit of hydrogenase 4 is crucial for regulating FOF1 dependent proton/potassium fluxes during fermentation of various concentrations of glucose

Escherichia coli anaerobically ferment glucose and perform proton/potassium exchange at pH 7.5. The role of hyf (hydrogenase 4) subunits (HyfBDF) in sensing different concentrations of glucose (2 g L^-1 or 8 g L^-1) via regulating H⁺/K⁺ exchange was studied. HyfB, HyfD and HyfF part of a protein family of NADH-ubiquinone oxidoreductase ND2, ND4 and ND5 subunits is predicted to operate as proton pump. Specific growth rate was optimal in wild type and mutants grown on 2 g L^-1 glucose reaching ~ 0.8 h^-1. It was shown that in wild type cells proton but not potassium fluxes were stimulated ~ 1.7 fold reaching up to 1.95 mmol/min when cells were grown in the presence of 8 g L^-1 glucose. Interestingly, cells grown on peptone only had similar proton/potassium fluxes as grown on 2 g L^-1glucose. H⁺/K⁺ fluxes of the cells grown on 2 g L^-1 but not 8 g L^-1 glucose depend on externally added glucose concentration in the assays. DCCD-sensitive H⁺ fluxes were tripled and K⁺ fluxes doubled in wild type cells grown on 8 g L^-1 glucose compared to 2 g L^-1 when in the assays 2 g L^-1glucose was added. Interestingly, in hyfF mutant when cells were grown on 2 g L^-1glucose and in 2 g L^-1 assays DCCD-sensitive fluxes were not determined compared to wild type while in hyfD mutant it was doubled reaching up to 0.657 mmol/min. In hyf mutants DCCD-sensitive K⁺ fluxes were stimulated in hyfD and hyfF mutants compared to wild type but depend on external glucose concentration. DCCD-sensitive H⁺/K⁺ ratio was equal to ~ 2 except hyfF mutant grown and assayed on 2 g L^-1glucose while in 8 g L^-1 conditions role of hyfB and hyfD is considered. Taken together it can be concluded that Hyd-4 subunits (HyfBDF) play key role in sensing glucose concentration for regulation of DCCD-sensitive H⁺/K⁺ fluxes for maintaining proton motive force generation.

The role of Escherichia coli FhlA transcriptional activator in generation of proton motive force and FO F1 -ATPase activity at pH 7.5

Escherichia coli is able to utilize the mixture of carbon sources and produce molecular hydrogen (H₂ ) via formate hydrogen lyase (FHL) complexes. In current work role of transcriptional activator of formate regulon FhlA in generation of fermentation end products and proton motive force, N'N'-dicyclohexylcarbodiimide (DCCD)-sensitive ATPase activity at 20 and 72 hr growth during utilization of mixture of glucose, glycerol, and formate were investigated. It was shown that in fhlA mutant specific growth rate was ~1.5 fold lower compared to wt, while addition of DCCD abolished the growth in fhlA but not in wt. Formate was not utilized in fhlA mutant but wt cells simultaneously utilized formate with glucose. Glycerol utilization started earlier (from 2 hr) in fhlA than in wt. The DCCD-sensitive ATPase activity in wt cells membrane vesicles increased ~2 fold at 72 hr and was decreased 70% in fhlA. Addition of formate in the assays increased proton ATPase activity in wt and mutant strain. FhlA absence mainly affected the ΔpH but not ΔΨ component of Δp in the cells grown at 72 hr but not in 24 hr. The Δp in wt cells decreased from 24 to 72 hr of growth ~40 mV while in fhlA mutant it was stable. Taken together, it is suggested that FhlA regulates the concentration of fermentation end products and via influencing F_O F₁ -ATPase activity contributes to the proton motive force generation.

Metabolomic and kinetic investigations on the electricity-aided production of butanol by Clostridium pasteurianum strains

In this contribution, we studied the effect of electro-fermentation on the butanol production of Clostridium pasteurianum strains by a targeted metabolomics approach. Two strains were examined: an electrocompetent wild type strain (R525) and a mutant strain (dhaB mutant) lacking formation of 1,3-propanediol (PDO). The dhaB-negative strain was able to grow on glycerol without formation of PDO, but displayed a high initial intracellular NADH/NAD ratio which was lowered subsequently by upregulation of the butanol production pathway. Both strains showed a 3-5 fold increase of the intracellular NADH/NAD ratio when exposed to cathodic current in a bioelectrochemical system (BES). This drove an activation of the butanol pathway and resulted in a higher molar butanol to PDO ratio for the R525 strain. Nonetheless, macroscopic electron balances suggest that no significant amount of electrons derived from the BES was harvested by the cells. Overall, this work points out that electro-fermentation can be used to trigger metabolic pathways and improve product formation, even when the used microbe cannot be considered electroactive. Accordingly, further studies are required to unveil the underlying (regulatory) mechanisms.

Methanol-dependent Escherichia coli strains with a complete ribulose monophosphate cycle

Methanol is a biotechnologically promising substitute for food and feed substrates since it can be produced renewably from electricity, water and CO2. Although progress has been made towards establishing Escherichia coli as a platform organism for methanol conversion via the energy efficient ribulose monophosphate (RuMP) cycle, engineering strains that rely solely on methanol as a carbon source remains challenging. Here, we apply flux balance analysis to comprehensively identify methanol-dependent strains with high potential for adaptive laboratory evolution. We further investigate two out of 1200 candidate strains, one with a deletion of fructose-1,6-bisphosphatase (fbp) and another with triosephosphate isomerase (tpiA) deleted. In contrast to previous reported methanol-dependent strains, both feature a complete RuMP cycle and incorporate methanol to a high degree, with up to 31 and 99% fractional incorporation into RuMP cycle metabolites. These strains represent ideal starting points for evolution towards a fully methylotrophic lifestyle.

Importance of consideration of oxidoreduction potential as a critical quality parameter in food industries

There are many intrinsic and extrinsic factors affecting the nutritional, organoleptic, microbial-enzymatic and physicochemical characteristics of food products. Some of these factors are commonly considered by food processors such as the temperature, water activity, pH, dissolved oxygen and chemical composition, while others are less considered such as the oxidoreduction potential (E_h). This latter factor is an intrinsic electrochemical parameter expressing the tendency of the substance/medium to give or receive electrons. Contrary to what is expected, the important role of E_h is not limited to inorganic chemistry, metallic chemistry, natural water, and wastewater treatment fields but it also covers many domains in biology such as metabolic engineering, enzymatic functions, food safety, and biotechnology. Unfortunately, although the critical roles of E_h in several key reactions occurred in biological media such as food and biotechnological products, its application or controlling is still uncommon or mis-considered by food processors. The lack of specific studies and reviews concerning the E_h and its influences on the quality parameters of products could be a reason for this lack of interest from the side of food processors. Recent studies reported the potential application of this parameter in novel food processing techniques such as reducing atmosphere drying (RAD) of food products and reducing atmosphere packaging (RAP) of fresh food products for preserving the quality attributes and extending the shelf-life of food products. This paper aims to help the technical and operational personnel working in food industry sectors as well as the scientific community to have an updated and a comprehensible review about the E_h parameter permitting its consideration for potential applications in food industries.

Enhanced volatile fatty acids production from anaerobic fermentation of food waste: A mini-review focusing on acidogenic metabolic pathways

Recently, efficient disposal of food waste (FW) with potential resource recovery has attracted great attentions. Due to its easily biodegradable nature, rich nutrient availability and high moisture content, FW is regarded as favorable substrate for anaerobic digestion (AD). Both waste disposal and energy recovery can be fulfilled during AD of FW. Volatile fatty acids (VFAs) which are the products of the first-two stages of AD, are widely applied in chemical industry as platform chemicals recently. Concentration and distribution of VFAs is the result of acidogenic metabolic pathways, which can be affected by the micro-environment (e.g. pH) in the digester. Hence, the clear elucidation of the acidogenic metabolic pathways is essential for optimization of acidogenic process for efficient product recovery. This review summarizes major acidogenic metabolic pathways and regulating strategies for enhancing VFAs recovery during acidogenic fermentation of FW.

Role of oxygen supply in α, ω-dodecanedioic acid biosynthesis from n-dodecane by Candida viswanathii ipe-1: Effect of stirring speed and aeration

α, ω-Dodecanedioic acid (DC₁₂) usually serves as a monomer of polyamides or some special nylons. During the biosynthesis, oxygenation cascaded in conversion of hydrophobic n-dodecane to DC₁₂, while the oxidation of n-dodecane took place in the intracellular space. Therefore, it was important to investigate the role of oxygen supply on the cell growth and DC₁₂ biosynthesis. It was found that stirring speed and aeration influenced the dissolved oxygen (DO) concentration which in turn affected cell growth as well as DC₁₂ biosynthesis. However, the effect of culture redox potential (Orp) level on DC₁₂ biosynthesis was more significant than that of DO level. For DC₁₂ biosynthesis, the first step was to form the emulsion droplets through the interaction of n-dodecane and the cell. When the stirring speed was enhanced, slits in the surface layer of the emulsion droplets would be increased. Thus, the substances transportation by water through the slits would be intensified, leading to an enhanced DC₁₂ production. Compared with the batch culture at a lower stirring speed (400 rpm) without culture redox potential (Orp) control, the DC₁₂ concentration was increased by 5 times up to 201.3 g/L with Orp controlled above 0 mV at a higher stirring speed (800 rpm).

Changing oxidoreduction potential to improve water-soluble yellow pigment production with Monascus ruber CGMCC 10910

Background

Monascus pigments are widely used in the food and pharmaceutical industries due to their safety to human health. Our previous study found that glucose concentration induced extracellular oxidoreduction potential (ORP) changes could influence extracellular water-soluble yellow pigment production by Monascus ruber CGMCC 10910 in submerged fermentation. In this study, H₂O₂ and dithiothreitol (DTT) were used to change the oxidoreduction potential for investigating the effects of oxidative or reductive substances on Monascus yellow pigment production by Monascus ruber CGMCC 10910.

Results

The extracellular ORP could be controlled by H₂O₂ and DTT. Both cell growth and extracellular water-soluble yellow pigment production were enhanced under H₂O₂-induced oxidative (HIO) conditions and were inhibited under dithiothreitol-induced reductive conditions. By optimizing the amount of H₂O₂ added and the timing of the addition, the yield of extracellular water-soluble yellow pigments significantly increased and reached a maximum of 209 AU, when 10 mM H₂O₂ was added on the 3rd day of fermentation with M. ruber CGMCC 10910. Under HIO conditions, the ratio of NADH/NAD+ was much lower than that in the control group, and the expression levels of relative pigment biosynthesis genes were up-regulated; moreover, the activity of glucose-6-phosphate dehydrogenase (G6PDH) was increased while 6-phosphofructokinase (PFK) activity was inhibited.

Conclusions

Oxidative conditions induced by H₂O₂ increased water-soluble yellow pigment accumulation via up-regulation of the expression levels of relative genes and by increasing the precursors of pigment biosynthesis through redirection of metabolic flux. In contrast, reductive conditions induced by dithiothreitol inhibited yellow pigment accumulation. This experiment provides a potential strategy for improving the production of Monascus yellow pigments.

Electronic supplementary material

The online version of this article (10.1186/s12934-017-0828-0) contains supplementary material, which is available to authorized users.

Artificial consortium that produces riboflavin regulates distribution of acetoin and 2,3-butanediol by Paenibacillus polymyxa CJX518

The introduction of an NADH/NAD⁺ regeneration system can regulate the distribution between acetoin and 2,3-butanediol. NADH regeneration can also enhance butanol production in coculture fermentation. In this work, a novel artificial consortium of Paenibacillus polymyxa CJX518 and recombinant Escherichia coli LS02T that produces riboflavin (VB₂) was used to regulate the NADH/NAD⁺ ratio and, consequently, the distribution of acetoin and 2,3-butanediol by P. polymyxa. Compared with a pure culture of P. polymyxa, the level of acetoin was increased 76.7% in the P. polymyxa and recombinant E. coli coculture. Meanwhile, the maximum production and yield of acetoin in an artificial consortium with fed-batch fermentation were 57.2 g/L and 0.4 g/g glucose, respectively. Additionally, the VB₂ production of recombinant E. coli could maintain a relatively low NADH/NAD⁺ ratio by changing NADH dehydrogenase activity. It was also found that 2,3-butanediol dehydrogenase activity was enhanced and improved acetoin production by the addition of exogenous VB₂ or by being in the artificial consortium that produces VB₂. These results illustrate that the coculture of P. polymyxa and recombinant E. coli has enormous potential to improve acetoin production. It was also a novel strategy to regulate the NADH/NAD⁺ ratio to improve the acetoin production of P. polymyxa.

Challenges in simulating the human gut for understanding the role of the microbiota in obesity

There is an elevated incidence of cases of obesity worldwide. Therefore, the development of strategies to tackle this condition is of vital importance. This review focuses on the necessity of optimising in vitro systems to model human colonic fermentation in obese subjects. This may allow to increase the resolution and the physiological relevance of the information obtained from this type of studies when evaluating the potential role that the human gut microbiota plays in obesity. In light of the parameters that are currently used for the in vitro simulation of the human gut (which are mostly based on information derived from healthy subjects) and the possible difference with an obese condition, we propose to revise and improve specific standard operating procedures.

Natural inactivation of Escherichia coli in anaerobic and reduced groundwater

AIMS

Inactivation rates of Escherichia coli in groundwater have most often been determined in aerobic and oxidized systems. This study examined E. coli inactivation rates in anaerobic and extremely reduced groundwater systems that have been identified as recharge zones.

METHODS AND RESULTS

Groundwater from six artesian wells was diverted to above-ground, flow-through mesocosms that contained laboratory grown E. coli in diffusion chambers. All groundwater was anaerobic and extremely reduced (ORP < -300 mV). Cells were plated onto mTEC agar during 21-day incubation periods. All data fit a bi-phasic inactivation model, with >95% of the E. coli population being inactivated <11·0 h (mean k = 0·488 ±0·188 h(-1) ).

CONCLUSIONS

The groundwater geochemical conditions enhanced the inactivation of E. coli to rates approx. 21-fold greater than previously published inactivation rate in groundwater (mean k = 0·023 ± 0·030 h(-1) ). Also, mTEC agar inhibits E. coli growth following exposure to anaerobic and reduced groundwater.

SIGNIFICANCE AND IMPACT OF THE STUDY

Aquifer recharge zones with geochemical characteristics observed in this study complement above-ground engineered processes (e.g. filtration, disinfection), while increasing the overall indicator micro-organism log-reduction rate of a facility.

Insights into the global regulation of anaerobic metabolism for improved biohydrogen production

To improve the biohydrogen yield in bacterial dark fermentation, a new approach of global anaerobic regulation was introduced. Two cellular global regulators FNR and NarP were overexpressed in two model organisms: facultatively anaerobic Enterobacter aerogenes (Ea) and strictly anaerobic Clostridium paraputrificum (Cp). The overexpression of FNR and NarP greatly altered anaerobic metabolism and increased the hydrogen yield by 40%. Metabolic analysis showed that the global regulation caused more reducing environment inside the cell. To get a thorough understanding of the global metabolic regulation, more genes (fdhF, fhlA, ppk, Cb-fdh1, and Sc-fdh1) were overexpressed in different Ea and Cp mutants. For the first time, it demonstrated that there were approximately linear relationships between the relative change of hydrogen yield and the relative change of NADH yield or ATP yield. It implied that cellular reducing power and energy level played vital roles in the biohydrogen production.

Fermentative Pyruvate and Acetyl-Coenzyme A Metabolism

Pyruvate and acetyl-CoA form the backbone of central metabolism. The nonoxidative cleavage of pyruvate to acetyl-CoA and formate by the glycyl radical enzyme pyruvate formate lyase is one of the signature reactions of mixed-acid fermentation in enterobacteria. Under these conditions, formic acid accounts for up to one-third of the carbon derived from glucose. The further metabolism of acetyl-CoA to acetate via acetyl-phosphate catalyzed by phosphotransacetylase and acetate kinase is an exemplar of substrate-level phosphorylation. Acetyl-CoA can also be used as an acceptor of the reducing equivalents generated during glycolysis, whereby ethanol is formed by the polymeric acetaldehyde/alcohol dehydrogenase (AdhE) enzyme. The metabolism of acetyl-CoA via either the acetate or the ethanol branches is governed by the cellular demand for ATP and the necessity to reoxidize NADH. Consequently, in the absence of an electron acceptor mutants lacking either branch of acetyl-CoA metabolism fail to cleave pyruvate, despite the presence of PFL, and instead reduce it to D-lactate by the D-lactate dehydrogenase. The conversion of PFL to the active, radical-bearing species is controlled by a radical-SAM enzyme, PFL-activase. All of these reactions are regulated in response to the prevalent cellular NADH:NAD+ ratio. In contrast to Escherichia coli and Salmonella species, some genera of enterobacteria, e.g., Klebsiella and Enterobacter, produce the more neutral product 2,3-butanediol and considerable amounts of CO2 as fermentation products. In these bacteria, two molecules of pyruvate are converted to α-acetolactate (AL) by α-acetolactate synthase (ALS). AL is then decarboxylated and subsequently reduced to the product 2,3-butandiol.

Enhanced poly(γ-glutamic acid) production by H2 O2 -induced reactive oxygen species in the fermentation of Bacillus subtilis NX-2

Effects of reactive oxygen species (ROS) on cell growth and poly(γ-glutamic acid) (γ-PGA) synthesis were studied by adding hydrogen peroxide to a medium of Bacillus subtilis NX-2. After optimizing the addition concentration and time of H₂ O₂ , a maximum concentration of 33.9 g/L γ-PGA was obtained by adding 100 µM H₂ O₂ to the medium after 24 H. This concentration was 20.6% higher than that of the control. The addition of diphenyleneiodonium chloride (ROS inhibitor) can interdict the effect of H₂ O₂ -induced ROS. Transcriptional levels of the cofactors and relevant genes were also determined under ROS stress to illustrate the possible metabolic mechanism contributing to the improve γ-PGA production. The transcriptional levels of genes belonging to the tricarboxylic acid cycle and electron transfer chain system were significantly increased by ROS, which decreased the NADH/NAD⁺ ratio and increased the ATP levels, thereby providing more reducing power and energy for γ-PGA biosynthesis. The enhanced γ-PGA synthetic genes also directly promoted the formation of γ-PGA. This study was the first to use the ROS control strategy for γ-PGA fermentation and provided valuable information on the possible mechanism by which ROS regulated γ-PGA biosynthesis in B. subtilis NX-2.

Improved propionic acid production with metabolically engineered Propionibacterium jensenii by an oxidoreduction potential-shift control strategy

In this study, a three-stage oxidoreduction potential (ORP) control strategy was developed to improve propionic acid (PA) production using engineered Propionibacterium jensenii ATCC 4868 (pZGX04-gldA) in a 3-L bioreactor. Specifically, ORP was controlled at -200mV from 0 to 36h, -300mV from 36 to 156h, and -400mV after 156h. The PA titer increased from 21.38 to 27.31g/L. The effects of ORP regulation on key intracellular metabolites were studied, demonstrating that ORP can both regulate NADH/NAD(+) ratio and the activities of some enzymes involved in electron transport and redistribute metabolic flux. We integrated the ORP control strategy with a fed-batch culture method and increased PA production to 39.53g/L. This new ORP control strategy may be useful in the optimization of other anaerobic processes.

Regulation of extracellular oxidoreduction potential enhanced (R,R)-2,3-butanediol production by Paenibacillus polymyxa CJX518

Cellular redox status and oxygen availability influence the product formation. Herein, decreasing agitation speed or adding vitamin C (Vc) achieved the 2,3-BDL yield of 0.40 g g(-1) or 0.39 g g(-1)glucose under batch fermentation, respectively. To our knowledge, this is the highest 2,3-BDL yield reported so far for Paenibacillus polymyxa without adding acetic acid. The NADH/NAD(+) ratio and 2,3-BDL titer could be increased significantly by reducing the agitation speed or adding Vc, indicating that the enhancement of 2,3-BDL is closely associated with the adjustment of NADH/NAD(+) ratio. Especially, Vc addition elevated the 2,3-BDL titer from 43.66 g L(-1) to 71.71 g L(-1) within 54 h under fed-batch fermentation. This is the highest titer of 2,3-BDL so far reported for P. polymyxa from glucose fermentation. This work provides a new strategy to improve 2,3-BDL production and helps us to understand the responses of P. polymyxa to extracellular oxidoreduction potential.

Suitable extracellular oxidoreduction potential inhibit rex regulation and effect central carbon and energy metabolism in Saccharopolyspora spinosa

Background

Polyketides, such as spinosad, are mainly synthesized in the stationary phase of the fermentation. The synthesis of these compounds requires many primary metabolites, such as acetyl-CoA, propinyl-CoA, NADPH, and succinyl-CoA. Their synthesis is also significantly influenced by NADH/NAD⁺. Rex is the sensor of NADH/NAD⁺ redox state, whose structure is under the control of NADH/NAD⁺ ratio. The structure of rex controls the expression of many NADH dehydrogenases genes and cytochrome bd genes. Intracellular redox state can be influenced by adding extracellular electron acceptor H₂O₂. The effect of extracellular oxidoreduction potential on spinosad production has not been studied. Although extracellular oxidoreduction potential is an important environment effect in polyketides production, it has always been overlooked. Thus, it is important to study the effect of extracellular oxidoreduction potential on Saccharopolyspora spinosa growth and spinosad production.

Results

During stationary phase, S. spinosa was cultured under oxidative (H₂O₂) and reductive (dithiothreitol) conditions. The results show that the yield of spinosad and pseudoaglycone increased 3.11 fold under oxidative condition. As H₂O₂ can be served as extracellular electron acceptor, the ratios of NADH/NAD⁺ were measured. We found that the ratio of NADH/NAD⁺ under oxidative condition was much lower than that in the control group. The expression of cytA and cytB in the rex mutant indicated that the expression of these two genes was controlled by rex, and it was not activated under oxidative condition. Enzyme activities of PFK, ICDH, and G6PDH and metabolites results indicated that more metabolic flux flow through spinosad synthesis.

Conclusion

The regulation function of rex was inhibited by adding extracellular electron acceptor-H₂O₂ in the stationary phase. Under this condition, many NADH dehydrogenases which were used to balance NADH/NAD⁺ by converting useful metabolites to useless metabolites and unefficient terminal oxidases (cytochrome bd) were not expressed. So lots of metabolites were not waste to balance. As a result, un-wasted metabolites related to spinosad and PSA synthesis resulted in a high production of spinosad and PSA under oxidative condition.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-014-0098-z) contains supplementary material, which is available to authorized users.

Effects of H2 and electrochemical reducing power on metabolite production by Clostridium acetobutylicum KCTC1037

A conventional fermenter (CF), a single-cathode fermenter (SCF), and a double-cathode fermenter (DCF) were employed to evaluate and compare the effects of H2 and electrochemical reducing power on metabolite production by Clostridium acetobutylicum KCTC1037. The source of the external reducing power for CF was H2, for the SCF was electrochemically reduced neutral red-modified graphite felt electrode (NR-GF), and for the DCF was electrochemically reduced combination of NR-GF and platinum plate electrodes (NR-GF/PtP). The metabolites produced from glucose or CO2 by strain KCTC1037 cultivated in the DCF were butyrate, ethanol, and butanol, but ethanol and butanol were not produced from glucose or CO2 by strain KCTC1037 cultivated in the CF and SCF. It is possible that electrochemically reduced NR-GF/PtP is a more effective source of internal and external reducing power than H2 or NR-GF for strain KCTC1037 to produce metabolites from glucose and CO2. This research might prove useful in developing fermentation technology to actualize direct bioalcohol production of fermentation bacteria from CO2.

Metabolic changes in Klebsiella oxytoca in response to low oxidoreduction potential, as revealed by comparative proteomic profiling integrated with flux balance analysis

Oxidoreduction potential (ORP) is an important physiological parameter for biochemical production in anaerobic or microaerobic processes. However, the effect of ORP on cellular physiology remains largely unknown, which hampers the design of engineering strategies targeting proteins associated with ORP response. Here we characterized the effect of altering ORP in a 1,3-propanediol producer, Klebsiella oxytoca, by comparative proteomic profiling combined with flux balance analysis. Decreasing the extracellular ORP from -150 to -240 mV retarded cell growth and enhanced 1,3-propanediol production. Comparative proteomic analysis identified 61 differentially expressed proteins, mainly involved in carbohydrate catabolism, cellular constituent biosynthesis, and reductive stress response. A hypothetical oxidoreductase (HOR) that catalyzes 1,3-propanediol production was markedly upregulated, while proteins involved in biomass precursor synthesis were downregulated. As revealed by subsequent flux balance analysis, low ORP induced a metabolic shift from glycerol oxidation to reduction and rebalancing of redox and energy metabolism. From the integrated protein expression profiles and flux distributions, we can construct a rational analytic framework that elucidates how (facultative) anaerobes respond to extracellular ORP changes.

Enhancement of succinate production by metabolically engineered Escherichia coli with co-expression of nicotinic acid phosphoribosyltransferase and pyruvate carboxylase

Escherichia coli BA002, in which the ldhA and pflB genes are deleted, cannot utilize glucose anaerobically due to the inability to regenerate NAD(+). To restore glucose utilization, overexpression of nicotinic acid phosphoribosyltransferase (NAPRTase) encoded by the pncB gene, a rate-limiting enzyme of NAD(H) synthesis pathway, resulted in a significant increase in cell mass and succinate production under anaerobic conditions. However, a high concentration of pyruvate accumulated. Thus, co-expression of NAPRTase and the heterologous pyruvate carboxylase (PYC) of Lactococcus lactis subsp. cremoris NZ9000 in recombinant E. coli BA016 was investigated. The total concentration of NAD(H) was 9.8-fold higher in BA016 than in BA002, and the NADH/NAD(+) ratio decreased from 0.60 to 0.04. Under anaerobic conditions, BA016 consumed 17.50 g l(-1) glucose and produced 14.08 g l(-1) succinate with a small quantity of pyruvate. Furthermore, when the reducing agent dithiothreitol or reduced carbon source sorbitol was added, the cell growth and carbon source consumption rate of BA016 was reasonably enhanced and succinate productivity increased.

Increasing reducing power output (NADH) of glucose catabolism for reduction of xylose to xylitol by genetically engineered Escherichia coli AI05

Anaerobic homofermentative production of reduced products requires additional reducing power (NADH and/or NADPH) output from glucose catabolism. Previously, with an anaerobically expressed pyruvate dehydrogenase operon (aceEF-lpd), we doubled the reducing power output to four NADH per glucose (or 1.2 xylose) catabolized anaerobically, which satisfied the NADH requirement to establish a non-transgenic homoethanol pathway (1 glucose or 1.2 xylose --> 2 acetyl-CoA + 4 NADH --> 2 ethanol) in the engineered strain, Escherichia coli SZ420 (∆frdBC ∆ldhA ∆ackA ∆focA-pflB ∆pdhR::pflBp6-pflBrbs-aceEF-lpd). In this study, E. coli SZ420 was further engineered for reduction of xylose to xylitol by (1) deleting the alcohol dehydrogenase gene (adhE) to divert NADH from the ethanol pathway; (2) deleting the glucose-specific PTS permease gene (ptsG) to eliminate catabolite repression and allow simultaneous uptake of glucose and xylose; (3) cloning the aldose reductase gene (xylI) of Candida boidinii to reduce xylose to xylitol. The resulting strain, E. coli AI05 (pAGI02), could in theory simultaneously uptake glucose and xylose, and utilize glucose as a source of reducing power for the reduction of xylose to xylitol, with an expected yield of four xylitol for each glucose consumed (YRPG = 4) under anaerobic conditions. In resting cell fermentation tests using glucose and xylose mixtures, E. coli AI05 (pAGI02) achieved an actual YRPG value of ~3.6, with xylitol as the major fermentation product and acetate as the by-product.

Systems-level characterization and engineering of oxidative stress tolerance in Escherichia coli under anaerobic conditions

Despite many prior studies on microbial response to oxidative stress, our understanding of microbial tolerance against oxidative stress is currently limited to aerobic conditions, and few engineering strategies have been devised to resolve toxicity issues of oxidative stress under anaerobic conditions. Since biological processes, such as anaerobic fermentation, are frequently hampered by toxicity arising from oxidative stress, increased microbial tolerance against oxidative stress improves the overall productivity and yield of biological processes. Here, we show a systems-level analysis of oxidative stress response of Escherichia coli under anaerobic conditions, and present an engineering strategy to improve oxidative stress tolerance. First, we identified essential cellular mechanisms and regulatory factors underlying oxidative stress response under anaerobic conditions using a transcriptome analysis. In particular, we showed that nitrogen metabolisms and respiratory pathways were differentially regulated in response to oxidative stress under anaerobic and aerobic conditions. Further, we demonstrated that among transcription factors with oxidative stress-derived perturbed activity, the deletion of arcA and arcB significantly improved oxidative stress tolerance under aerobic and anaerobic conditions, respectively, whereas fnr was identified as an essential transcription factor for oxidative stress tolerance under anaerobic conditions. Moreover, we showed that oxidative stress increased the intracellular NADH : NAD(+) ratio under aerobic and anaerobic conditions, which indicates a regulatory role of NADH in oxidative stress tolerance. Based on this finding, we demonstrated that increased NADH availability through fdh1 overexpression significantly improved oxidative stress tolerance under aerobic conditions. Our results here provide novel insight into better understanding of cellular mechanisms underlying oxidative stress tolerance under anaerobic conditions, and into developing strain engineering strategies to enhance microbial tolerance against oxidative stress towards improved biological processes.